Interpretive Summary: Mycobacteria are a type of bacteria that are capable of infecting and causing disease in animals. Johne’s disease is caused by a subgroup of mycobacteria and results in severe economic losses within the dairy industry. The identification of infected animals is difficult due to the large amount of other mycobacteria that are present in the environment but do not generally cause disease. This research identified differences in the DNA of mycobacteria that were collected from a variety of different animals. These differences can be used to design improved diagnostic tests as well as help scientists understand why some mycobacteria are capable of causing disease in animals while others do not. This work will be of primary interest to other scientists.

Technical Abstract:
A comparative genomic approach was used to identify large sequence polymorphisms among Mycobacterium avium (M. avium) subspecies obtained from a variety of host animals. DNA microarrays were used as a platform for comparing mycobacterial isolates with the sequenced bovine isolate M. avium subsp. paratuberculosis K-10. Open reading frames (ORFs) were classified as present or divergent based on the relative fluorescent intensities of the experimental samples compared to M. avium subsp. paratuberculosis K-10 DNA. Three large deletions were observed in the genomes of M. avium subsp. paratuberculosis isolates obtained from sheep and four clusters of ORFs homologous to sequences in the M. avium subsp. avium 104 genome were identified as being present in these isolates. One of these clusters encodes glycopeptidolipid biosynthesis enzymes which have not previously been identified in M. avium subsp. paratuberculosis. M. avium subsp. silvaticum isolates could be distinguished from the other mycobacterial isolates based on their unique hybridization profile. This group also included a sheep isolates as well as four independent laboratory stocks of the organism traditionally identified as M. avium subsp. avium strain 18. Two cattle isolates and one sheep isolate had genome profiles similar to M. avium subsp. avium 104, while isolates obtained from cattle (n = 5), birds (n = 4), goats (n = 3), bison (n = 3), and humans (n = 9) were indistinguishable from M. avium subsp. paratuberculosis K-10. Genome diversity in M. avium subspecies appears to be mediated by large sequence polymorphisms that are commonly associated with mobile genetic elements.